Higher-order inputs provide important regulatory control to motor circuits, but few cellular-level studies of such inputs have been performed. To begin studying higher-order neurons in an accessible model system, we have localized, in the supraesophageal ganglion (brain), neurons that are candidates for influencing the well-characterized motor circuits in the stomatogastric nervous system (STNS) of the crab Cancer borealis. The STNS is an extension of the central nervous system and includes four ganglia, within which are a set of motor circuits that regulate the ingestion and processing of food. These motor circuits are locally regulated by a set of modulatory neurons, most of which are located in the paired commissural ganglia (CoGs). These modulatory neurons are well-positioned to receive input from brain neurons because the circumesophageal commissures (CoCs) connect the brain with the CoGs. We have performed a series of CoC backfills to localize the brain neurons that are likely to innervate the CoGs and are, therefore, candidates for influencing the STNS motor patterns. CoC backfill-labeled neuronal somata within the brain are clustered around a subset of anatomically defined neuropil regions. We have concomitantly localized many CoG neurons that project into the brain. This latter pathway presumably includes neurons that provide feedback regarding ongoing STNS activity. Interestingly, nearly all of these brain and CoG neurons project through the medial aspect of the CoC. This work provides an initial framework for future studies to determine the way that higher-order input regulates rhythmic motor patterns.